Predicting Enzyme鈥揝ubstrate Specificity with QM/MM Methods: A Case Study of the Stereospecificity of d-Glucarate Dehydratase

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• 作者：Boxue Tian ; Frank Wallrapp ; Chakrapani Kalyanaraman ; Suwen Zhao ; Leif A. Eriksson ; Matthew P. Jacobson
• 刊名：Biochemistry
• 出版年：2013
• 出版时间：August 20, 2013
• 年：2013
• 卷：52
• 期：33
• 页码：5511-5513
• 全文大小：196K
• 年卷期：v.52,no.33(August 20, 2013)
• ISSN：1520-4995

文摘

The stereospecificity of d-glucarate dehydratase (GlucD) is explored by QM/MM calculations. Both the substrate binding and the chemical steps of GlucD contribute to substrate specificity. Although the identification of transition states remains computationally intensive, we suggest that QM/MM computations on ground states or intermediates can capture aspects of specificity that cannot be obtained using docking or molecular mechanics methods.